CN116590429A - SNP molecular marker related to pig reproduction traits and pig breeding and application thereof - Google Patents
SNP molecular marker related to pig reproduction traits and pig breeding and application thereof Download PDFInfo
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- 230000001488 breeding effect Effects 0.000 title claims abstract description 25
- 230000001850 reproductive effect Effects 0.000 claims abstract description 23
- 101100135737 Sus scrofa PCCB gene Proteins 0.000 claims abstract description 11
- 238000000034 method Methods 0.000 claims abstract description 9
- 239000002773 nucleotide Substances 0.000 claims abstract description 9
- 125000003729 nucleotide group Chemical group 0.000 claims abstract description 9
- 238000012216 screening Methods 0.000 claims abstract description 9
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- 108091028043 Nucleic acid sequence Proteins 0.000 claims abstract description 3
- 241000282887 Suidae Species 0.000 claims description 14
- 108700028369 Alleles Proteins 0.000 claims description 13
- 108020004414 DNA Proteins 0.000 claims description 13
- 238000012163 sequencing technique Methods 0.000 claims description 6
- 238000012408 PCR amplification Methods 0.000 claims description 4
- 238000011144 upstream manufacturing Methods 0.000 claims description 4
- 238000004458 analytical method Methods 0.000 claims description 3
- 241000282898 Sus scrofa Species 0.000 claims 5
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- 238000009394 selective breeding Methods 0.000 abstract 1
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- 238000000605 extraction Methods 0.000 description 3
- 238000000246 agarose gel electrophoresis Methods 0.000 description 2
- HVYWMOMLDIMFJA-DPAQBDIFSA-N cholesterol Chemical compound C1C=C2C[C@@H](O)CC[C@]2(C)[C@@H]2[C@@H]1[C@@H]1CC[C@H]([C@H](C)CCCC(C)C)[C@@]1(C)CC2 HVYWMOMLDIMFJA-DPAQBDIFSA-N 0.000 description 2
- 239000000203 mixture Substances 0.000 description 2
- 238000000746 purification Methods 0.000 description 2
- 210000001519 tissue Anatomy 0.000 description 2
- 238000007400 DNA extraction Methods 0.000 description 1
- 201000001431 Hyperuricemia Diseases 0.000 description 1
- 241001465754 Metazoa Species 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 238000012098 association analyses Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 235000012000 cholesterol Nutrition 0.000 description 1
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Abstract
The invention discloses a SNP molecular marker related to pig reproduction traits and pig breeding and application thereof, and relates to the technical field of pig molecular markers. The propagation characters are total number of born and healthy number of born; the molecular marker is positioned in a partial DNA sequence of the pig PCCB gene, the nucleotide sequence of the molecular marker is shown as a sequence table SEQ ID NO.1, and the length of the sequence is 713bp; the molecular marker comprises SNP of an rs345310133 locus; there was a C/T base mutation at 387bp of the sequence. The invention discovers that one SNP molecular marker in the pig PCCB gene is related to the total number of piglets and the healthy number of piglets, so that the invention can be used for pig marker assisted selective breeding, namely provides a new application of one SNP molecular marker in the pig PCCB gene in marker assisted breeding of pig reproductive traits, and realizes early screening of pig reproductive traits, and the screening method is simple and rapid.
Description
Technical Field
The invention relates to the technical field of pig molecular markers, in particular to a SNP molecular marker related to pig reproduction traits and pig breeding.
Background
Genetic improvement of pig reproductive traits is increasingly receiving attention from breeders. The total litter size and the healthy litter size are several important indexes for evaluating the reproductive traits of pigs, and the improvement of the total litter size and the healthy litter size of pigs has great significance for improving the overall economic benefit of the pig industry. However, since the reproductive traits of pigs are low genetic traits, about 0.1, the conventional breeding improvement is difficult. Therefore, the molecular marker affecting the reproductive trait is searched, and the molecular assisted breeding has important significance for improving pig reproduction.
The PCCB gene (PCCB) is located on chromosome 13 of pig and is involved in the decomposition of lipid, cholesterol and amino acids, and mutation of the gene causes the hyperuricemia. At present, no report on SNP loci related to the PCCB gene and the pig reproductive traits exists, so that the discovery of the marker has potential important value for genetic improvement of the pig reproductive traits.
Disclosure of Invention
The invention aims to overcome the defects of the prior art and provides an SNP molecular marker related to pig reproduction traits and pig breeding and application thereof.
In order to achieve the technical purpose, the invention mainly adopts the following technical scheme:
in a first aspect, the present invention provides a SNP molecular marker associated with porcine reproductive traits, both total litter size and healthy litter size, and porcine breeding; the molecular marker is positioned in a partial DNA sequence of the pig PCCB gene, the nucleotide sequence of the molecular marker is shown as a sequence table SEQ ID NO.1, and the length of the sequence is 713bp; the molecular marker comprises SNP of an rs345310133 locus; there was a C/T base mutation at 387bp of the sequence.
Further, the nucleotide polymorphism site of C or T at 387bp in the sequence SEQ ID NO.1 is expressed as three genotypes of CC, CT or TT, wherein the T allele is a dominant allele.
In a second aspect, the invention provides the use of a SNP molecular marker as set forth in the first aspect in screening of porcine reproductive traits and breeding of pigs.
In a third aspect, the present invention provides a primer pair for amplifying a molecular marker as described in the first aspect, the primer pair comprising: the nucleotide sequence of the upstream primer is shown as SEQ ID NO.2, and the nucleotide sequence of the downstream primer is shown as SEQ ID NO. 3.
In a fourth aspect, the invention provides the use of a primer pair as described in the third aspect in screening for porcine reproductive traits and breeding pigs.
In a fifth aspect, the invention provides a kit for rapid breeding using SNP molecular markers associated with porcine reproductive traits and porcine breeding as described in the first aspect, comprising a primer pair as described in the third aspect.
In a sixth aspect, the present invention provides a method for pig breeding, the method comprising:
s1, extracting genome DNA of a pig;
s2, carrying out PCR amplification by using the genomic DNA obtained in the step S1 as a template and adopting the primer pair as defined in claim 4 to obtain the molecular marker as defined in claim 1 and purifying;
s3, carrying out sequencing analysis on the molecular marker purified in the step S2, reserving individuals carrying T alleles at 387bp of the sequence, and eliminating individuals carrying C alleles.
Preferably, in step S1, genomic DNA is extracted from the ear border tissue of the pig to be tested.
Compared with the prior art, the invention has the beneficial effects that: the invention discovers that one SNP molecular marker (rs 345310133) in the pig PCCB gene is related to the reproductive trait of the pig, in particular to the total litter size and the healthy litter size trait for the first time, so that the molecular marker can be used for screening the reproductive trait of the pig and breeding, namely, the invention provides a new application of one SNP molecular marker in the pig PCCB gene in the marker-assisted breeding of the reproductive trait of the pig, and realizes the early screening of the reproductive trait of the pig, and the screening method is simple and rapid.
Drawings
FIG. 1 is a diagram showing agarose gel electrophoresis detection of a PCR product in example 1 of the present invention, wherein lane M is DL2000 Marker, lanes 1-3 are amplified fragments in black pigs, and the fragment size is 713bp;
FIG. 2 is a sequencing map of g.77221540C > T locus in example 1 of the invention;
Detailed Description
The technical solutions of the present invention will be clearly and completely described below in conjunction with the embodiments of the present invention, and it is apparent that the described embodiments are only some embodiments of the present invention, not all embodiments. All other embodiments, which can be made by one of ordinary skill in the art without undue burden on the person of ordinary skill in the art based on embodiments of the present invention, are within the scope of the present invention.
Example 1 acquisition of pig PCCB Gene SNP detection fragment and establishment of method for detecting polymorphic site
1. Extraction of pig genomic DNA
The test pig breed of the invention is big white pig, and the extraction of pig genome DNA adopts an animal tissue genome DNA extraction kit (PureLink) produced by Invitrogen company TM Pro 96Genomic DNA Purification Kit,K182104A), and the pig genomic DNA was extracted according to the kit instructions. And (3) detecting the concentration and quality of the extracted DNA, and storing at-20 ℃ for standby.
2. Acquisition of pig PCCB gene SNP genetic marker detection fragment
(1) PCR amplification
A pair of primers is designed according to the SNP genetic marker detection sequence (shown as SEQ ID NO. 1) in the genome sequence (GenBank ID: NC-010447) of the pig PCCB gene, and fragments of the polymorphic site are amplified. The primers were as follows:
an upstream primer: 5'AGACCCTTCACAAAGCCTGC 3'
A downstream primer: 5'GTCAGAGGCACCTTGCACA 3'
By using the primers and taking the genome DNA of the large white pig as a template, carrying out PCR amplification, wherein the PCR reaction system comprises 50 mu L, and the components in the system are as follows: 100ng of genomic DNA, 25. Mu.L of PCR mix, 1. Mu.L of each of the above upstream and downstream primers, and ddH 2 O was made up to a total volume of 50. Mu.L.
The PCR was run as follows: pre-denaturation at 94℃for 3min; denaturation at 94℃for 30s, annealing at 58℃for 30s, elongation at 72℃for 30s,35 cycles; extending at 72 ℃ for 10min; preserving at 4 ℃. The PCR product was detected by 1.5% agarose gel electrophoresis, the detection result is shown in FIG. 1, wherein lane M is DL2000 Marker, lanes 1-3 are amplified fragments in big white pigs, the amplified fragments have the size of 713bp, and the sequence is shown in SEQ ID NO. 1.
SEQ ID NO.1:
AGACCCTTCACAAAGCCTGCTTTAGGTTTCCACCTCCTGCTTCTCCATTCTTCTTTTTGTTGCTCCTTAGGTCTCTAGTAATGTTTATGGAACTAGTTACCTTGTTCCAAGGTCAGGCTCTCCTTACCCCCACGTCTCTCCGGCTTTCCCTCCTACTCTTTTATTTGCCTTCCACGTTAGTGACTCCTGGAGCAGCCTTGGTATCCTTGCTGGCTTAATTCTACTGGTAACTCTTGTCTCTTGGGCAGGATGATGGAATATAGGCTTTCACATGGGGCGGAGGCAAAATCAGCCCTCCTGGCCCTCCCATGACATCACTAAGTGATTTTTGTTGCATTTTAGGGAAAGCTAACGGCCAGAGAACGGATCAGTCTCTTGCTGGACCCCGGCAGTTTTATTGAGAGTGACATGTTTGTGGAACACAGATGTGCAGATTTTGGAATGGCTGCTGACAAGAATAAGGTATCTGTTCACAGTGGTGGTACAAGCCTACAAATTACCCGTAGCAGCTATGGCCCTGCTGGCCTACCCAATAGACAAATGAAGTTCTTCCAGGACTCAGGATACATTGAAAACTTTTCAAGGGTGGGGCCCTGGAATTCTCAAAGTGCCTATTGAGAAGCACTATTGGGGCCTCCCGGTTCCCACTCACCTTTGTCTGCAGATGAAGAATATGGGTAGCCAGCCTATACCTTGTGCAAGGTGCCTCTGAC。
(2) PCR product purification
The PCR amplified product was purified using a Gel Extraction Kit kit from Shanghai Biotechnology Co., ltd, and specific steps are shown in the kit specification.
3. Detection of molecular markers by direct sequencing of PCR products
The PCR purified product obtained above is directly sent to Beijing Oreg company for sequencing, and the genotype of the site in the detection population is judged according to the sequencing result. Analysis using SeqMan software revealed that there was a C > T allele mutation at 387bp in the sequence, i.e., g.10953632C > T, which caused the polymorphism of the PCCB gene, as shown in FIG. 2.
EXAMPLE 2 detection of polymorphism distribution of molecular markers in white pigs
In this example, the polymorphism distribution rule of the PCCB gene g.10953632C > T site of pigs was detected in 1100 large white pigs, and the detection results are shown in Table 1.
TABLE 1 distribution law of polymorphism of PCCB gene g.10953632C > T site
From the results in Table 1, it can be seen that: the PCCB gene g.10953632C > T site in large white pigs is represented by three genotypes of CC, CT and TT, wherein the CC genotypes are more individuals, and the CC allele frequency is 56.27%.
Example 3 correlation analysis of molecular markers and porcine reproductive traits
In order to determine whether the pig PCCB gene g.109532C > T locus is related to the difference of pig reproduction traits, polymorphism detection is performed by the method established in example 1, and the correlation of different genotypes of the polymorphic locus with the pig total litter size and litter size traits is analyzed. And performing association analysis on the mutation sites by adopting a GLM model of SAS 19.0 software. The adopted model is as follows:
Y ijk =μ+G i +A j +S k +e ijk ,
wherein: y is Y ijk Representing a table value; mu represents population mean; g i Indicating genotypic effects; a is that j Representing a year season effect; s is S k Representing the parent effect; e, e ijk Representing the random residual effect. P (P)<0.05, the difference is judged to be significant; p (P)<0.01 is judged to be extremely different.
Correlation analysis among different genotypes, total litter size and litter size traits was performed in large white pigs, and the statistical analysis results are shown in table 2:
TABLE 2 correlation analysis of PCCB Gene g.10953632C > T site and porcine reproductive characteristics
Note that: the mean composition in the table was mean ± standard deviation, a and B representing the difference was very significant (P < 0.01).
As can be seen from Table 2, in large white pigs, the total litter size and litter size of TT genotype individuals at g.109532C > T locus are significantly higher than those of CC genotype individuals (P < 0.01), so that the T allele is the dominant allele and individuals carrying this dominant allele should be maintained in breeding, thereby contributing to an increase in the overall litter size and litter size traits of the population.
The present invention is not limited to the above-mentioned embodiments, and any changes or substitutions that can be easily understood by those skilled in the art within the technical scope of the present invention are intended to be included in the scope of the present invention.
Claims (8)
1. A SNP molecular marker associated with porcine reproductive traits and porcine breeding, characterized in that the reproductive traits are total litter size and healthy litter size; the molecular marker is positioned in a partial DNA sequence of the pig PCCB gene, the nucleotide sequence of the molecular marker is shown as a sequence table SEQ ID NO.1, and the length of the sequence is 713bp; the molecular marker comprises SNP of an rs345310133 locus; there was a C/T base mutation at 387bp of the sequence.
2. The SNP molecular marker associated with porcine reproductive traits and porcine breeding according to claim 1, wherein the nucleotide polymorphism site of C or T at 387bp in sequence SEQ ID No.1 is represented as three genotypes CC, CT or TT, wherein the T allele is a dominant allele.
3. The use of the SNP molecular markers of claim 1 or 2 in pig breeding trait screening and pig breeding.
4. A primer pair for amplifying the molecular marker of claim 1, wherein the primer pair comprises: the nucleotide sequence of the upstream primer is shown as SEQ ID NO.2, and the nucleotide sequence of the downstream primer is shown as SEQ ID NO. 3.
5. The use of the primer pair according to claim 4 in screening for porcine reproductive traits and in breeding pigs.
6. A kit for rapid breeding using the SNP molecular markers associated with porcine reproductive traits and porcine breeding according to claim 1, comprising the primer pair of claim 4.
7. A method for pig breeding, the method comprising:
s1, extracting genome DNA of a pig;
s2, carrying out PCR amplification by using the genomic DNA obtained in the step S1 as a template and adopting the primer pair as defined in claim 4 to obtain the molecular marker as defined in claim 1 and purifying;
s3, carrying out sequencing analysis on the molecular marker purified in the step S2, reserving individuals carrying T alleles at 387bp of the sequence, and eliminating individuals carrying C alleles.
8. The method according to claim 7, wherein in step S1, genomic DNA is extracted from the ear margin tissue of the swine to be tested.
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